Contacts of the helix formed by residues 211 - 225 (chain A) in PDB entry 3OFN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 211 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLN* 1.3 86.2 - - - +
212A ARG* 1.3 63.6 + - - +
213A SER* 3.1 29.1 + - - +
214A THR* 3.2 22.9 + - - +
215A VAL* 3.6 13.7 + - - +
237A THR* 4.0 0.3 - - - +
238A ALA* 4.4 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LYS* 1.3 71.8 - - - +
213A SER* 1.3 61.7 + - - +
214A THR 3.1 1.6 - - - -
215A VAL* 3.0 6.2 + - + +
216A ALA* 2.8 28.8 + - - +
237A THR* 3.3 35.6 + - + +
239A SER* 3.8 21.6 + - - -
240A GLU* 3.9 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LYS* 3.1 32.1 + - - +
212A ARG* 1.3 77.3 - - - +
214A THR* 1.3 56.8 + - - +
216A ALA* 3.6 8.8 - - - +
217A GLN* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLN* 3.2 23.8 - - + +
211A LYS* 3.2 39.8 + - - +
212A ARG 3.1 0.8 - - - -
213A SER* 1.3 79.6 + - - +
215A VAL* 1.3 56.9 + - - +
217A GLN* 3.2 6.1 + - - +
218A LEU* 2.9 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 5.0 4.7 - - + -
117A ILE* 6.2 0.4 - - + -
205A TYR* 5.7 1.3 - - + -
207A ALA* 3.6 28.5 - - + -
210A GLN* 3.8 12.6 - - + +
211A LYS 3.6 14.8 + - - +
212A ARG* 3.0 8.6 + - + +
214A THR* 1.3 72.1 - - - +
216A ALA* 1.3 61.6 + - - +
218A LEU* 3.2 9.3 + - + +
219A VAL* 2.9 35.1 + - + +
233A ILE* 4.2 25.1 - - + -
235A ALA* 4.3 11.9 - - + -
237A THR* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ARG 2.8 16.2 + - - +
213A SER* 3.6 10.8 - - - +
215A VAL* 1.3 77.1 - - - +
217A GLN* 1.3 62.9 + - - +
219A VAL* 3.3 6.2 + - - +
220A GLN* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A SER 2.9 20.1 + - - +
214A THR* 3.7 5.4 - - - +
216A ALA* 1.3 73.2 - - - +
218A LEU* 1.3 57.5 + - - +
220A GLN* 3.1 34.9 + - - +
221A THR* 2.8 53.1 + - - +
224A GLN* 4.3 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 4.3 19.1 - - + -
182A LEU* 3.9 34.1 - - + -
205A TYR* 3.4 45.3 - - + +
210A GLN* 6.1 0.2 - - - +
214A THR* 2.9 17.4 + - + +
215A VAL* 3.5 12.6 - - + +
217A GLN* 1.3 76.3 - - - +
219A VAL* 1.3 63.8 + - + +
221A THR* 2.9 17.5 + - - -
222A LEU* 3.0 18.3 + - + +
233A ILE* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 3.7 30.5 - - + -
215A VAL* 2.9 33.1 + - + +
216A ALA* 3.6 6.1 - - - +
218A LEU* 1.3 73.6 - - + +
220A GLN* 1.3 62.9 + - - +
221A THR 3.3 0.2 + - - -
222A LEU* 3.3 1.6 + - - -
223A GLU* 3.1 36.5 + - - +
228A MET* 3.4 23.3 - - + +
233A ILE* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ALA* 3.0 20.6 + - - +
217A GLN* 3.1 35.0 + - - +
219A VAL* 1.3 78.4 - - - +
221A THR* 1.3 56.6 + - - +
223A GLU* 3.3 13.5 + - - +
224A GLN* 2.9 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 4.5 12.6 - - + -
186A LEU* 5.6 1.3 - - + -
217A GLN* 2.8 31.6 + - - +
218A LEU* 2.9 9.6 + - - -
220A GLN* 1.3 72.3 - - - +
222A LEU* 1.3 64.9 + - - +
224A GLN* 3.3 10.2 + - + +
225A HIS* 3.0 44.8 + - + +
435A TYR* 3.7 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 3.5 28.9 - - + -
185A ILE* 3.9 26.9 - - + -
186A LEU* 4.5 2.2 - - + -
205A TYR* 5.7 1.1 - - + -
218A LEU* 3.0 20.8 + - + +
219A VAL* 3.7 5.6 - - - +
221A THR* 1.3 75.2 - - - +
223A GLU* 1.3 55.8 + - - +
225A HIS* 3.2 4.2 - - - -
226A ASP 2.9 8.8 + - - -
227A ALA* 2.7 39.0 + - + -
228A MET* 3.4 33.7 - - + +
231A SER* 4.2 14.8 - - - +
233A ILE* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS* 5.1 9.9 + - - -
219A VAL* 3.1 28.5 + - - +
220A GLN* 3.4 16.8 - - - +
222A LEU* 1.3 75.3 - - - +
224A GLN* 1.3 64.0 + - + +
226A ASP* 3.0 14.5 + - - +
228A MET* 3.8 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 4.3 10.5 - - - +
220A GLN* 2.9 44.5 + - + +
221A THR* 3.5 10.9 - - - +
223A GLU* 1.3 75.5 - - + +
225A HIS* 1.3 71.9 + - + +
226A ASP* 3.4 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 3.6 30.3 - - + -
189A LYS* 2.7 36.3 + - - +
221A THR* 3.0 33.4 + - + +
222A LEU 3.2 0.7 - - - +
224A GLN* 1.3 87.7 - - + +
226A ASP* 1.3 66.2 + - - +
227A ALA* 2.9 5.5 + - - +
435A TYR* 3.5 37.0 + + + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il